Locus 3647

Sequence ID 2R_DroMel_CAF1
Location 12,101,099 – 12,101,299
Length 200
Max. P 0.994085
window5936 window5937 window5938

overview

Window 6

Location 12,101,099 – 12,101,219
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 94.67
Mean single sequence MFE -50.38
Consensus MFE -41.58
Energy contribution -42.38
Covariance contribution 0.80
Combinations/Pair 1.11
Mean z-score -1.48
Structure conservation index 0.83
SVM decision value 0.29
SVM RNA-class probability 0.672201
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 12101099 120 - 20766785
UCCUUGAUGACCUUGGUCAGACGCUCGGCGUCGACCUCAACGCCCACAGAGCUGAGGAUCUUCUCCAGAUCGCUGUUGGCGGGCGAGUCCUUGCCACCGAGGACGGCCAGAAGGUAAGCA
....((...(((((((((.(((((...)))))))))....((((.((((..(((..(.....)..)))....)))).))))(((..(((((((....))))))).)))..)))))...)) ( -50.90)
>DroSec_CAF1 5393 120 - 1
UCCUUGAUGACCUUGGUCAGACGCUCGGCGUCAACCUCAACGCCCACGGAGCUGAGGAUCUUCUCCAGAUCGCCGUUGGCGGGCGAGUCCUUGCCACCGAGGACGGCCAGAAGGUAAGCA
....((...(((((((((.(((((...)))))..((((..((((.((((..(((..(.....)..)))....)))).))))(((((....)))))...))))..)))))..))))...)) ( -51.20)
>DroSim_CAF1 5374 120 - 1
UCCUUGAUGACCUUGGUCAGACGCUCGGCGUCGACCUCAACGCCCACGGAGCUGAGGAUCUUCUCCAGAUCGCCGUUGGCGGGCGAGUCCUUGCCACCGAGGACGGCCAGAACGUAAGCA
..(((.(((.....((((.(((((...)))))))))((..((((.((((..(((..(.....)..)))....)))).))))(((..(((((((....))))))).))).)).)))))).. ( -48.10)
>DroEre_CAF1 5610 120 - 1
UCCUUGAUGACCUUGGUCAGGCGCUCGGUGUCGACCUCGAUGCCCACAGAGCUGAGGAUCUUCUCCAGGUCGGCGUUGGCGGGGGAGUCCUUGCCACCGAGGACGGCCAGAAGGUAAGCA
.((((..((((....))))...(((((((((((....)))))))....)))).))))(((((((...(((((.((.((((((((....)))))))).))....))))))))))))..... ( -51.20)
>DroYak_CAF1 5782 120 - 1
UCCUUGAUGACCUUGGUCAGGCGCUCAGCGUCGACCUCAAUGCCCACAGAGCUGAGGAUCUUCUCCAGGUCGGCGUUGGCGGGGGUGUCCUUGCCACCGAGGACGGCCAGAAGGUAAGCA
.((((..((((....))))..(((.((((((((((((....((.......))...(((.....)))))))))))))))))).((.((((((((....)))))))).))..))))...... ( -50.50)
>consensus
UCCUUGAUGACCUUGGUCAGACGCUCGGCGUCGACCUCAACGCCCACAGAGCUGAGGAUCUUCUCCAGAUCGCCGUUGGCGGGCGAGUCCUUGCCACCGAGGACGGCCAGAAGGUAAGCA
....((...(((((((((.(((((...)))))..((((..((((.((((..(((..(.....)..)))....)))).))))(((((....)))))...))))..)))))..))))...)) (-41.58 = -42.38 +   0.80)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 7

Location 12,101,179 – 12,101,299
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 95.67
Mean single sequence MFE -52.50
Consensus MFE -45.92
Energy contribution -46.36
Covariance contribution 0.44
Combinations/Pair 1.08
Mean z-score -1.64
Structure conservation index 0.87
SVM decision value 1.24
SVM RNA-class probability 0.934677
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 12101179 120 + 20766785
UUGAGGUCGACGCCGAGCGUCUGACCAAGGUCAUCAAGGAGCUGGCUGGCAAGAGCAUCGACGACCUGAUCAAGGAGGGUCGCGAGAAGCUCUCCUCGAUGCCGGUGGGCGGCGGUGGUG
....(((((((((...))))).)))).....(((((..(.(((.((((((((((((.(((.((((((.........)))))))))...)))))......))))))).)))..)..))))) ( -53.60)
>DroSec_CAF1 5473 120 + 1
UUGAGGUUGACGCCGAGCGUCUGACCAAGGUCAUCAAGGAGCUGGCUGGCAAGAGCAUCGACGACCUGAUCAAGGAGGGUCGCGAGAAGCUCUCCUCGAUGCCGGUGGGCGGCGGUGGUG
....(((((((((...))))).)))).....(((((..(.(((.((((((((((((.(((.((((((.........)))))))))...)))))......))))))).)))..)..))))) ( -51.50)
>DroSim_CAF1 5454 120 + 1
UUGAGGUCGACGCCGAGCGUCUGACCAAGGUCAUCAAGGAGCUGGCUGGCAAGAGCAUCGACGACCUGAUCAAGGAGGGUCGCGAGAAGCUCUCCUCGAUGCCGGUGGGCGGCGGUGGUG
....(((((((((...))))).)))).....(((((..(.(((.((((((((((((.(((.((((((.........)))))))))...)))))......))))))).)))..)..))))) ( -53.60)
>DroEre_CAF1 5690 120 + 1
UCGAGGUCGACACCGAGCGCCUGACCAAGGUCAUCAAGGAGCUGGCUGGCAAGAGCAUCGAGGACCUCAUCAAGGAGGGACGCGAGAAGCUCUCCUCGAUGCCGGUGGGCGGCGGUGGCG
(((....)))(((((..(((((.(((..((.((((.(((((((....)))..((((.(((.(..((((......))))..).)))...)))))))).)))))))))))))).)))))... ( -55.20)
>DroYak_CAF1 5862 120 + 1
UUGAGGUCGACGCUGAGCGCCUGACCAAGGUCAUCAAGGAGCUGGCUGGCAAGAGCAUCGAGGAGCUCAUCAAGCAGGGACGCGAGAAGCUCUCCUCGAUGCCGGUGGGCGGCGGUGGUG
..........((((.(.((((((((....)))).......(((.(((((((......((((((((..(.((..((......))..)).)..))))))))))))))).))))))).))))) ( -48.60)
>consensus
UUGAGGUCGACGCCGAGCGUCUGACCAAGGUCAUCAAGGAGCUGGCUGGCAAGAGCAUCGACGACCUGAUCAAGGAGGGUCGCGAGAAGCUCUCCUCGAUGCCGGUGGGCGGCGGUGGUG
..........(((((..(((((.(((..((.((((.(((((((....)))..((((.(((.((((((.........)))))))))...)))))))).)))))))))))))).)))))... (-45.92 = -46.36 +   0.44)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 8

Location 12,101,179 – 12,101,299
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 95.67
Mean single sequence MFE -45.70
Consensus MFE -40.54
Energy contribution -41.14
Covariance contribution 0.60
Combinations/Pair 1.05
Mean z-score -2.03
Structure conservation index 0.89
SVM decision value 2.45
SVM RNA-class probability 0.994085
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 12101179 120 - 20766785
CACCACCGCCGCCCACCGGCAUCGAGGAGAGCUUCUCGCGACCCUCCUUGAUCAGGUCGUCGAUGCUCUUGCCAGCCAGCUCCUUGAUGACCUUGGUCAGACGCUCGGCGUCGACCUCAA
.......((((.....))))(((((((((.((.....))....))))))))).((((((((((.(((..........)))...)))))))))).((((.(((((...))))))))).... ( -45.80)
>DroSec_CAF1 5473 120 - 1
CACCACCGCCGCCCACCGGCAUCGAGGAGAGCUUCUCGCGACCCUCCUUGAUCAGGUCGUCGAUGCUCUUGCCAGCCAGCUCCUUGAUGACCUUGGUCAGACGCUCGGCGUCAACCUCAA
.((((..((((.....))))(((((((((.((.....))....))))))))).((((((((((.(((..........)))...))))))))))))))..(((((...)))))........ ( -42.70)
>DroSim_CAF1 5454 120 - 1
CACCACCGCCGCCCACCGGCAUCGAGGAGAGCUUCUCGCGACCCUCCUUGAUCAGGUCGUCGAUGCUCUUGCCAGCCAGCUCCUUGAUGACCUUGGUCAGACGCUCGGCGUCGACCUCAA
.......((((.....))))(((((((((.((.....))....))))))))).((((((((((.(((..........)))...)))))))))).((((.(((((...))))))))).... ( -45.80)
>DroEre_CAF1 5690 120 - 1
CGCCACCGCCGCCCACCGGCAUCGAGGAGAGCUUCUCGCGUCCCUCCUUGAUGAGGUCCUCGAUGCUCUUGCCAGCCAGCUCCUUGAUGACCUUGGUCAGGCGCUCGGUGUCGACCUCGA
((.(((((.((((.((((((((((((((((((...(((.(..((((......))))..).))).))))..((......))))))))))).))..)))..))))..))))).))....... ( -50.30)
>DroYak_CAF1 5862 120 - 1
CACCACCGCCGCCCACCGGCAUCGAGGAGAGCUUCUCGCGUCCCUGCUUGAUGAGCUCCUCGAUGCUCUUGCCAGCCAGCUCCUUGAUGACCUUGGUCAGGCGCUCAGCGUCGACCUCAA
.......((((.....))))...((((.((((((.(((.((....)).))).)))))).((((((((..((((((....))......((((....))))))))...)))))))))))).. ( -43.90)
>consensus
CACCACCGCCGCCCACCGGCAUCGAGGAGAGCUUCUCGCGACCCUCCUUGAUCAGGUCGUCGAUGCUCUUGCCAGCCAGCUCCUUGAUGACCUUGGUCAGACGCUCGGCGUCGACCUCAA
.......((((.....))))(((((((((.((.....))....))))))))).((((((((((.(((..........)))...)))))))))).((((.(((((...))))))))).... (-40.54 = -41.14 +   0.60)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:00:48 2006